EMIGRANT, Mont. — Rain fell on empty fishing access parking lots along the Yellowstone River on Friday morning. The river looked like chocolate milk — fishing was going to be tough. Inside Angler’s West, a fly shop here not far from the river, Rick Wollum answered a phone call.

“It’s open, but it’s dirty,” Wollum told the caller.

The murky water put a bit of a damper on what was an otherwise happy occasion for Wollum and other anglers and river users throughout the Paradise Valley, reported the Bozeman Daily Chronicle (http://bit.ly/2di20yv). It was the first day in the last month that people were allowed to access whatever section of the river they wanted. It was a long time coming, but few took advantage, leaving the river looking about as quiet as it was over the last month.

A little more than a month ago, Montana Fish, Wildlife and Parks shut down all water-based recreation on this river and its tributaries from the border with Yellowstone National Park downstream to the town of Laurel. It was a response to an outbreak of a parasite that biologists say killed tens of thousands of mountain whitefish.

The microscopic parasite causes proliferative kidney disease, and is believed to be new in the Yellowstone system. State biologists said low flows and high water temperatures likely made the parasite even more devastating for the Yellowstone’s whitefish, and that the closure was necessary to prevent the spread of the parasite and to reduce stress on the fish.

But as late summer flirted with fall, river temperatures cooled and biologists stopped seeing so many fish dying. Section by section, the river was reopened. And now, people can use the entire river however they want. Life will be allowed to return to normal. Businesses that took a hit when the river closed will lick their wounds and can begin trying to recover from their losses, and FWP biologists will begin planning how they will try to measure the overall impact.

“What I’d like to see is FWP answer the question of to what extent is the population damaged,” said Pat Byorth, the director of Trout Unlimited’s Montana Water Project.

Throughout the fish kill, FWP officials said they assumed they were only seeing about 10 percent of all the dead fish, if that. Agency staff saw more than 4,000 dead whitefish and a handful of trout, but they didn’t see the ones that floated ahead of them, or that sunk to the bottom. FWP’s regional fisheries manager Travis Horton has said he expects the impact to the population to be fairly significant, but it’s going to be hard for them to answer how significant it is.

They won’t be able to offer a grand total of dead fish, but they can try to figure out what the population looks like. With trout, some of which were affected by the parasite, they will be able to compare population numbers from next spring to numbers gathered this past spring.

But with whitefish, that’s going to be a lot tougher. Data on the species is far scarcer. They aren’t exactly sure what the Yellowstone River’s whitefish population looked like before the fish kill.

“Ideally we’d like to have a quality estimate that we could go and look at,” Horton said. “But we don’t have that.”

Old and weak

Mountain whitefish are native to Montana, but the species has always taken a backseat to the almighty trout. Anglers prefer big browns and rainbows to the snout-nosed whiteys. The hierarchy is evident even in the data Montana’s state wildlife agency has collected over the years.

Trout per-mile estimates are done regularly on most major rivers in the state, but the same is not true of whitefish. Estimates have been done, but not nearly as frequently as for trout. On the Yellowstone River, the most recent per-mile numbers for whitefish are 13 years old.

Biologists sampled whitefish on the Yellowstone in certain sections in 1999, 2001 and 2003, and the numbers are eye-popping. A few stretches of river in the Paradise Valley are listed as having more than 10,000 whitefish per mile.

Those numbers jive with what people have always thought; that there are a lot of whitefish in the Yellowstone. Some think those numbers mean the fish kill is going to be a minor speed bump, that nobody will notice any impact to the population. Some think the real problem is that FWP stopped looking at the scaly salmonids.

“The real tragedy is that they quit counting them,” said John Bailey, the owner of Dan Bailey’s Fly Shop in Livingston.

But Scott Opitz, FWP’s Yellowstone River area biologist, said they stopped gathering the data because the estimates contained inherent biases that caused them to balloon.

“There was just some real question as to the value of having those estimates when you couldn’t really stand behind them,” Opitz said.

Per-mile estimates are arrived at through a method called mark and recapture. That means electrofishing crews float a river section two separate times. On the first run, they mark all the fish they catch so they can be recognized later. On the second run, usually a week or two later, the crews catch some of the same fish and some new ones.

The estimates hinge on the comparison of the two figures — the new captures and the recaptures. But if the recapture rate is too low, the estimates are considered unreliable because it can inflate the final figure and leave a wide range of variability. The length of the river section they sample on can throw off the recapture rates, too. If it is too short, fish can move around and escape crews on their recapture run.

Low recapture rates and the length of the river section are two reasons FWP doesn’t put much faith in the old population numbers.

One estimate done in the Mill Creek area in 1999 found there were 10,837 whitefish per mile there, but David Schmetterling, a research coordinator with FWP, said there were several problems with it. Samples were taken on just a half mile of stream, rather than the standard of a couple of miles. On the first run, crews caught and marked 299 whitefish. On the second run, they caught 511, but only 20 of them were marked, which Schmetterling said was too low to be reliable. And the potential range for the estimate was between 8,027 and 19,368, leaving a lot of room for variability.

Problems like that plagued most of the Yellowstone River whitefish estimates done between 1999 and 2003, said Schmetterling.

“I think these are all over-estimates of population size,” Schmetterling said.

FWP realized that at the time, and so they stopped doing the estimates. Now, though, the old data will have renewed relevance as FWP tries to understand exactly what happened on the river this past August.

“It gives you a ballpark, and definitely a place to start,” Schmetterling said.

Though they don’t consider the per-mile estimates to be solid, the raw data that makes them up will prove useful. The electrofishing runs reflect the number of fish they handled, and they can recreate those runs. Where a number falls in comparison will be somewhat telling, especially if it is significantly higher or lower.

“That’s something we can easily do a followup with and have at least some level of comparison,” Opitz said.

Other options they are considering include trying to learn the distribution of fish of different sizes, which will give them a feel for whether any particular age class is missing from the population. They might also try out a genetic sampling technique that can tell them the number of breeding fish that contributed to the population. That method is still fairly new but might prove useful.

No matter what method they choose, though, they won’t instantly know everything they want.

“It’s going to take several years to get a handle on it,” Schmetterling said. “Next year will be the first of many.”

Studying the canary

When fishery biologists talk about whitefish, they often call them the “canary in the coal mine.” Struggling whitefish populations are considered a sign of larger troubles in the river system, but for so long, the fish were so abundant they were considered a nuisance by many trout-obsessives. Byorth said biologists didn’t think they needed to track their numbers.

“I don’t think we can rely on that anymore,” he said.

Some work is being done. The species was recently studied on the Madison River, and Schmetterling said parts of western Montana are starting to pay more attention to the species.

Opitz himself regularly samples the whitefish population on a portion of the Shields River, but he said time constraints and river conditions have historically made the work tough on the Yellowstone.

“Areas where we can do that we are doing it,” Opitz said. “It’s just the Yellowstone and the complications between sheer volumes of whitefish and flow regime to squeeze that in.”

Now, though, the focus will likely be renewed. Catastrophe can make things like that happen, especially in wildlife biology.

“Oftentimes, biological interest is in the rearview mirror, trying to figure out what happened,” Horton said.

The parasite that caused this outbreak isn’t going to disappear. In the Snake River system in eastern Idaho, the parasite is believed to be the culprit for five years of fish kills, all popping up around the same time of year. Each year the kill has lessened in intensity, which gives Montana’s biologists some hope that the fish will build some immunity to it.

But there’s no promise that will happen, and even if it does, fish will still be vulnerable to drought and high water temperatures, two other threats that aren’t expected to go away.

Byorth said helping fish succeed might rely on creating river conditions that will help them weather the worst environmental conditions. That could mean leaving more water in tributary streams, or changing how people build near the river. The idea is to control human activity in a way that gives fish a fighting chance.

“If each fish has a chance to thrive,” Byorth said, “then the population thrives.”

Information from: Bozeman Daily Chronicle, http://www.bozemandailychronicle.com